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- EMDB-39435: structure of phage T4 topoisomerase II central domain bound with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-39435
Titlestructure of phage T4 topoisomerase II central domain bound with DNA
Map dataT4 topo II map
Sample
  • Complex: Phage T4 topoisomerase II central domian bound with G-segment DNA
    • Protein or peptide: DNA topoisomerase medium subunit
    • Protein or peptide: phage T4 topoisomerase II gp39-gp60 subunit
    • DNA: DNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*TP*AP*TP*A)-3')
    • DNA: DNA (5'-D(P*AP*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*CP*AP*T)-3')
  • Ligand: MAGNESIUM ION
Keywordstopoisomerase II / ISOMERASE
Function / homology
Function and homology information


sister chromatid segregation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / protein-containing complex / DNA binding / ATP binding
Similarity search - Function
DNA topoisomerase II, eukaryotic-type / : / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA-like domain superfamily
Similarity search - Domain/homology
DNA topoisomerase medium subunit
Similarity search - Component
Biological speciesEscherichia phage T4 (virus) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChen YT / Xin YH / Xian RQ
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2024
Title: Structural and functional insights into the T-even type bacteriophage topoisomerase II.
Authors: Yuhui Xin / Runqi Xian / Yunge Yang / Jingyuan Cong / Zihe Rao / Xuemei Li / Yutao Chen /
Abstract: T-even type bacteriophages are virulent phages commonly used as model organisms, playing a crucial role in understanding various biological processes. One such process involves the regulation of DNA ...T-even type bacteriophages are virulent phages commonly used as model organisms, playing a crucial role in understanding various biological processes. One such process involves the regulation of DNA topology during phage replication upon host infection, governed by type IIA DNA topoisomerases. In spite of various studies on prokaryotic and eukaryotic counterparts, viral topoisomerase II remains insufficiently understood, especially the unique domain composition of T4 phage. In this study, we determine the cryo-EM structures of topoisomerase II from T4 and T6 phages, including full-length structures of both apo and DNA-binding states which have never been determined before. Together with other conformational states, these structures provide an explicit blueprint of mechanisms of phage topoisomerase II. Particularly, the asymmetric dimeric interactions observed in cryo-EM structures of T6 phage topoisomerase II ATPase domain and central domain bound with DNA shed light on the asynchronous ATP usage and asynchronous cleavage of the G-segment DNA, respectively. The elucidation of phage topoisomerase II's structures and functions not only enhances our understanding of mechanisms and evolutionary parallels with prokaryotic and eukaryotic homologs but also highlights its potential as a model for developing type IIA topoisomerase inhibitors.
History
DepositionMar 12, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39435.png

Downloads & links

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Map

FileDownload / File: emd_39435.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT4 topo II map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-3.143971 - 4.341508
Average (Standard dev.)0.0008398182 (±0.10389022)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: T4 topo II half map

Fileemd_39435_half_map_1.map
AnnotationT4 topo II half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: T4 topo II half map

Fileemd_39435_half_map_2.map
AnnotationT4 topo II half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Phage T4 topoisomerase II central domian bound with G-segment DNA

EntireName: Phage T4 topoisomerase II central domian bound with G-segment DNA
Components
  • Complex: Phage T4 topoisomerase II central domian bound with G-segment DNA
    • Protein or peptide: DNA topoisomerase medium subunit
    • Protein or peptide: phage T4 topoisomerase II gp39-gp60 subunit
    • DNA: DNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*TP*AP*TP*A)-3')
    • DNA: DNA (5'-D(P*AP*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*CP*AP*T)-3')
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Phage T4 topoisomerase II central domian bound with G-segment DNA

SupramoleculeName: Phage T4 topoisomerase II central domian bound with G-segment DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia phage T4 (virus)

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Macromolecule #1: DNA topoisomerase medium subunit

MacromoleculeName: DNA topoisomerase medium subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 51.951973 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQLNNRDLKS IIDNEALAYA MYTVENRAIP NMIDGFKPVQ RFVIARALDL ARGNKDKFHK LASIAGGVAD LGYHHGENSA QDAGALMAN TWNNNFPLLD GQGNFGSRTV QKAAASRYIF ARVSKNFYNV YKDTEYAPVH QDKEHIPPAF YLPIIPTVLL N GVSGIATG ...String:
MQLNNRDLKS IIDNEALAYA MYTVENRAIP NMIDGFKPVQ RFVIARALDL ARGNKDKFHK LASIAGGVAD LGYHHGENSA QDAGALMAN TWNNNFPLLD GQGNFGSRTV QKAAASRYIF ARVSKNFYNV YKDTEYAPVH QDKEHIPPAF YLPIIPTVLL N GVSGIATG YATYILPHSV SSVKKAVLQA LQGKKVTKPK VEFPEFRGEV VEIDGQYEIR GTYKFTSRTQ MHITEIPYKY DR ETYVSKI LDPLENKGFI TWDDACGEHG FGFKVKFRKE YSLSDNEEER HAKIMKDFGL IERRSQNITV INEKGKLQVY DNV VDLIKD FVEVRKTYVQ KRIDNKIKET ESAFRLAFAK AHFIKKVISG EIVVQGKTRK ELTEELSKID MYSSYVDKLV GMNI FHMTS DEAKKLAEEA KAKKEENEYW KTTDVVTEYT KDLEEIKHHH HHHHHHH

UniProtKB: DNA topoisomerase medium subunit

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Macromolecule #2: phage T4 topoisomerase II gp39-gp60 subunit

MacromoleculeName: phage T4 topoisomerase II gp39-gp60 subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 77.524703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIKNEIKILS DIEHIKKRSG MYIGSSANET HERFMFGKWE SVQYVPGLVK LIDEIIDNSV DEGIRTKFKF ANKINVTIKN NQVTVEDNG RGIPQAMVKT PTGEEIPGPV AAWTIPKAGG NFGDDKERVT GGMNGVGSSL TNIFSVMFVG ETGDGQNNIV V RCSNGMEN ...String:
MIKNEIKILS DIEHIKKRSG MYIGSSANET HERFMFGKWE SVQYVPGLVK LIDEIIDNSV DEGIRTKFKF ANKINVTIKN NQVTVEDNG RGIPQAMVKT PTGEEIPGPV AAWTIPKAGG NFGDDKERVT GGMNGVGSSL TNIFSVMFVG ETGDGQNNIV V RCSNGMEN KSWEDIPGKW KGTRVTFIPD FMSFETNELS QVYLDITLDR LQTLAVVYPD IQFTFNGKKV QGNFKKYARQ YD EHAIVQE QENCSIAVGR SPDGFRQLTY VNNIHTKNGG HHIDCAMDDI CEDLIPQIKR KFKIDVTKAR VKECLTIVMF VRD MKNMRL IRQTKERLTS PFGEIRSHIQ LDAKKISRDI LNNEAILMPI IEAALARKLA AEKAAETKAA KKASKAKVHK HIKA NLCGK DADTTLFLTE GDSAIGYLID VRDKELHGGY PLRGKVLNSW GMSYADMLKN KELFDICAIT GLVLGEKAFE EKEDG EWFT FELNGDTIIV NENDEVQING KWITVGELRK NLMKFVKIDS SSVDMKKYKL QNNVRRSIKS SSMNYANVAI MTDADH DGL GSIYPSLLGF FSNWPELFEQ GRIRFVKTPV IIAQVGKKQE WFYTVAEYES AKDALPKHSI RYIKGLGSLE KSEYREM IQ NPVYDVVKLP ENWKELFEML MGDNADLRKE WMSQHHHHHH

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Macromolecule #3: DNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP...

MacromoleculeName: DNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*TP*AP*TP*A)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 16.058391 KDa
SequenceString: (DA)(DT)(DG)(DC)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DG)(DT) (DA)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT) ...String:
(DA)(DT)(DG)(DC)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DG)(DT) (DA)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)

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Macromolecule #4: DNA (5'-D(P*AP*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP...

MacromoleculeName: DNA (5'-D(P*AP*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*CP*AP*T)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 15.965361 KDa
SequenceString: (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DG)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DC)(DA)(DT)(DA)(DC)(DA)(DT)(DA)(DT)(DA) (DC) (DA)(DT)(DA)(DT)(DA)(DT) ...String:
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DG)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DC)(DA)(DT)(DA)(DC)(DA)(DT)(DA)(DT)(DA) (DC) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DG)(DC)(DA)(DT)

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 269648
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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